The result also extended Bayern's unbeaten run against Freiburg in league meetings to 21 matches, with 17 wins and four draws.
The build-up was overshadowed by the news that Bayern coach Vincent Kompany had been taken to hospital after collapsing at the training ground on Friday. His coaching staff took charge of the team, with assistant Aaron Danks overseeing a successful afternoon as Bayern responded to Dortmund's victory over Eintracht Frankfurt.
Bayern took the lead in the 16th minute when Dayot Upamecano finished a swift counter-attack. After blocking a shot near his own penalty area, the defender continued his run and collected Michael Olise's pass before calmly slotting the ball into the bottom corner.
Serge Gnabry doubled the visitors' advantage shortly before half-time. The forward timed his run perfectly to meet Nathaniel Brown's through ball and fired a low finish past Freiburg goalkeeper Mio Backhaus.
Freiburg attempted to fight their way back into the contest after the break, with manager Julian Schuster making two substitutions before the hour mark. Igor Matanovic immediately threatened with a long-range effort that forced Bayern goalkeeper Jonas Urbig into action.
The hosts reduced the deficit in the 82nd minute when Bayern defender Tom Bischof inadvertently turned a dangerous cross into his own net. The goal set up a tense finish, but Urbig produced an excellent reaction save to deny Matthias Ginter, while Sacha Boey also had a goal ruled out.
Bayern finally secured the points when Olise capitalised on Backhaus being caught out of position, rolling a long-range effort into the unguarded net to complete the 3-1 win.
The victory lifted Bayern above Dortmund on goal difference, giving them the perfect boost ahead of Der Klassiker. Freiburg remain third but are now four points behind the league leaders.